I'm looking at the UCSC Genome Browser view of TP53 in GRCh38 and am trying to interpret the GENCODE intron/exon annotations. The documentation of display conventions explain the color codes of the track, but I also see one TP53 subtracks whose label is highlighted in black:
Is there any significance to this? What does it mean for a GENCODE subtrack label to be highlighted in black?
This highlighting is representing something different than the track display, which we may not be very clear about. What the highlighting in this case is showing is the transcript you selected from your search results.
You probably got here by searching for TP53 . If you click the first search result from that link, you'll see the third transcript highlighted (same as the picture you provided). You can try clicking others, and you'll see that it will highlight different ones.
If you look at the search results again, you'll notice some of these are in bold. These represent the canonical transcript for that gene, in this case it's the first hit.
So the bold hits in the search results are canonical, and then the highlighted item in hgTracks corresponds to your search selection.
If you have any additional questions, you can reach out to our help desk at email@example.com. We check Biostars every now and again, but your question may go unanswered for some time. If you post a question here, using the "ucsc" helps to put it on our radar.